KANSAS CITY — A court order to destroy bioengineered sugar beet seed root stock has created significant concern in the sugar industry and has further clouded future U.S. sugar beet production.

Judge Jeffrey White in the U.S. District Court for Northern California on Nov. 30 ordered root stock, or stecklings, currently growing in nurseries be “removed from the ground” as of Dec. 7. The stecklings would have been replanted next year to produce seed for use in 2012.

The order was part of an ongoing lawsuit filed in 2008 by the Center for Food Safety and others concerning the use of “Roundup Ready” sugar beet seeds from the Monsanto Co. that were approved by the U.S. Department of Agriculture in 2005. An estimated 95% of the 2010 U.S. sugar beet crop acreage was planted to the bioengineered seed.

It is unknown how much traditional sugar beet seed is available for next year’s crop. U.S.D.A. analysts have estimated total U.S. sugar production may fall by 20% without the bioengineered seeds. The U.S.D.A. estimated sugar from sugar beets accounted for 57% of U.S. sugar production in 2009-10, with 43% coming from sugar cane.

Industry analysts have estimated sugar produced from sugar beets may drop as much as 50% in 2012 (processed from the 2011 sugar beet crop), and that domestic refined sugar prices may skyrocket.

Some beet processors that had been booking sugar from prospective 2012 production have stopped offering sugar for that year pending a resolution to the case. One trader noted the latest court order “was not positive for beet growers.”

In August Judge White revoked the U.S.D.A.’s deregulation of the seeds and ordered a full environmental impact study, which the U.S.D.A. said will not be available until May 2012.

A draft environmental assessment from the U.S.D.A. was published in the Nov. 4 Federal Register and is available for public comment until Dec. 6.